Accelerating the Discovery of Anticancer Peptides through Deep Forest Architecture with Deep Graphical Representation

Lantian Yao, Wenshuo Li, Yuntian Zhang, Junyang Deng, Yuxuan Pang, Yixian Huang, Chia Ru Chung, Jinhan Yu, Ying Chih Chiang*, Tzong Yi Lee*

*此作品的通信作者

研究成果: Article同行評審

10 引文 斯高帕斯(Scopus)

摘要

Cancer is one of the leading diseases threatening human life and health worldwide. Peptide-based therapies have attracted much attention in recent years. Therefore, the precise prediction of anticancer peptides (ACPs) is crucial for discovering and designing novel cancer treatments. In this study, we proposed a novel machine learning framework (GRDF) that incorporates deep graphical representation and deep forest architecture for identifying ACPs. Specifically, GRDF extracts graphical features based on the physicochemical properties of peptides and integrates their evolutionary information along with binary profiles for constructing models. Moreover, we employ the deep forest algorithm, which adopts a layer-by-layer cascade architecture similar to deep neural networks, enabling excellent performance on small datasets but without complicated tuning of hyperparameters. The experiment shows GRDF exhibits state-of-the-art performance on two elaborate datasets (Set 1 and Set 2), achieving 77.12% accuracy and 77.54% F1-score on Set 1, as well as 94.10% accuracy and 94.15% F1-score on Set 2, exceeding existing ACP prediction methods. Our models exhibit greater robustness than the baseline algorithms commonly used for other sequence analysis tasks. In addition, GRDF is well-interpretable, enabling researchers to better understand the features of peptide sequences. The promising results demonstrate that GRDF is remarkably effective in identifying ACPs. Therefore, the framework presented in this study could assist researchers in facilitating the discovery of anticancer peptides and contribute to developing novel cancer treatments.

原文English
文章編號4328
期刊International Journal Of Molecular Sciences
24
發行號5
DOIs
出版狀態Published - 3月 2023

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